From e869d19688ee99dde44e0d79bcf464533ed217eb Mon Sep 17 00:00:00 2001 From: Orion Buske Date: Sat, 8 Nov 2014 18:54:53 -0500 Subject: [PATCH] Updated rST --- README.md | 18 +++++++++--------- 1 file changed, 9 insertions(+), 9 deletions(-) diff --git a/README.md b/README.md index 232569e..96d6a72 100644 --- a/README.md +++ b/README.md @@ -5,26 +5,26 @@ Pipelines for analyzing padlock-captured DNA sequencing data -1) Initial configuration: +## 1. Initial configuration: -a) Install necessary scripts (bowtie, bismark, trimmomatic): +### - Install necessary scripts (bowtie, bismark, trimmomatic): `$ make install` -b) Reference preparation: +### - Reference preparation: -- Download fasta files for reference genome into subdirectory of `sequences` folder (or symlink them) + * Download fasta files for reference genome into subdirectory of `sequences` folder (or symlink them) - e.g. `$ mkdir sequences/hg19; cd sequences/hg19; ln -s /path/to/hg19.fa` + e.g. `$ mkdir sequences/hg19; cd sequences/hg19; ln -s /path/to/hg19.fa` -- Prepare bismark genomic indexes: + * Prepare bismark genomic indexes: - `$ lib/bismark_v0.12.3/bismark_genome_preparation sequences/phiX` - `$ lib/bismark_v0.12.3/bismark_genome_preparation sequences/hg19` + `$ lib/bismark_v0.12.3/bismark_genome_preparation sequences/phiX` + `$ lib/bismark_v0.12.3/bismark_genome_preparation sequences/hg19` -2) Run pipeline on a sample directory (containing paired-end files of the form: `_L001_R1_001.fastq.gz`, `_L001_R2_001.fastq.gz`): +## 2. Run pipeline on a sample directory (containing paired-end files of the form: `_L001_R1_001.fastq.gz`, `_L001_R2_001.fastq.gz`): `$ src/bis_seq/run_sample.sh hg19 /path/to/sample/`